[English] 日本語
Yorodumi
- PDB-8oz0: Structure of a human 48S translation initiation complex with eIF4... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8oz0
TitleStructure of a human 48S translation initiation complex with eIF4F and eIF4A
Components
  • (40S ribosomal protein ...) x 30
  • (Eukaryotic translation initiation factor ...) x 18
  • 18S rRNA
  • 60S ribosomal protein L41
  • Eukaryotic initiation factor 4A-I
  • Receptor of activated protein C kinase 1
  • Small ribosomal subunit protein uS13
  • Ubiquitin-40S ribosomal protein S27a
  • mRNA
  • tRNAiMet
KeywordsTRANSLATION / eIF4A / eIF4F / initiation / ribosome / mRNA
Function / homology
Function and homology information


positive regulation of eukaryotic translation initiation factor 4F complex assembly / male germ cell proliferation / eukaryotic initiation factor eIF2 binding / positive regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to manganese-induced endoplasmic reticulum stress / viral translational termination-reinitiation ...positive regulation of eukaryotic translation initiation factor 4F complex assembly / male germ cell proliferation / eukaryotic initiation factor eIF2 binding / positive regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to manganese-induced endoplasmic reticulum stress / viral translational termination-reinitiation / Cellular response to mitochondrial stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / methionyl-initiator methionine tRNA binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / negative regulation of translational initiation in response to stress / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic initiation factor 4E binding / PERK-mediated unfolded protein response / eukaryotic translation initiation factor 3 complex, eIF3m / PERK regulates gene expression / response to kainic acid / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 2 complex / RNA cap binding / eukaryotic translation initiation factor 4F complex / nuclear stress granule / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / formation of cytoplasmic translation initiation complex / multi-eIF complex / regulation of translational initiation in response to stress / regulation of cellular response to stress / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / Deadenylation of mRNA / mRNA cap binding / formation of translation preinitiation complex / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 48S preinitiation complex / M-decay: degradation of maternal mRNAs by maternally stored factors / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of ubiquitin-protein transferase activity / regulation of translational initiation / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / protein-synthesizing GTPase / protein tyrosine kinase inhibitor activity / positive regulation of DNA-templated transcription initiation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nucleolus organization / TNFR1-mediated ceramide production / GDP-dissociation inhibitor activity / negative regulation of RNA splicing / positive regulation of protein localization to cell periphery / neural crest cell differentiation / metal-dependent deubiquitinase activity / supercoiled DNA binding / cytoplasmic translational initiation / NF-kappaB complex / negative regulation of DNA repair / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / rRNA modification in the nucleus and cytosol / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / ion channel inhibitor activity / protein kinase A binding / laminin receptor activity / Ribosomal scanning and start codon recognition / pigmentation / positive regulation of mitochondrial depolarization / Translation initiation complex formation / positive regulation of protein metabolic process / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / Protein hydroxylation / monocyte chemotaxis / BH3 domain binding / negative regulation of translational frameshifting / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / SARS-CoV-1 modulates host translation machinery / positive regulation of GTPase activity / mTORC1-mediated signalling / TOR signaling
Similarity search - Function
ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / EIF3I / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H ...ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / EIF3I / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor, beta propellor-like domain / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / : / Eukaryotic translation initiation factor eIF2A / eIF3 subunit 6 N terminal domain / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / EIF3CL-like, C-terminal domain / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / : / eIF3a, PCI domain, TPR-like region / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / : / Eukaryotic translation initiation factor 2 alpha subunit / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / DEAD-box RNA helicase Q motif profile. / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / S1 domain profile. / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature.
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 2 subunit 1 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 2 subunit 1 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Eukaryotic translation initiation factor 2 subunit 2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Eukaryotic translation initiation factor 2 subunit 3 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Eukaryotic translation initiation factor 1A, X-chromosomal / Eukaryotic translation initiation factor 5 / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic initiation factor 4A-I / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Eukaryotic translation initiation factor 4 gamma 1 / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBrito Querido, J. / Sokabe, M. / Diaz-Lopez, I. / Gordiyenko, Y. / Fraser, C.S. / Ramakrishnan, V.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM092927 United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A.
Authors: Jailson Brito Querido / Masaaki Sokabe / Irene Díaz-López / Yuliya Gordiyenko / Christopher S Fraser / V Ramakrishnan /
Abstract: Eukaryotic translation initiation involves recruitment of the 43S pre-initiation complex to the 5' end of mRNA by the cap-binding complex eIF4F, forming the 48S translation initiation complex (48S), ...Eukaryotic translation initiation involves recruitment of the 43S pre-initiation complex to the 5' end of mRNA by the cap-binding complex eIF4F, forming the 48S translation initiation complex (48S), which then scans along the mRNA until the start codon is recognized. We have previously shown that eIF4F binds near the mRNA exit channel of the 43S, leaving open the question of how mRNA secondary structure is removed as it enters the mRNA channel on the other side of the 40S subunit. Here we report the structure of a human 48S that shows that, in addition to the eIF4A that is part of eIF4F, there is a second eIF4A helicase bound at the mRNA entry site, which could unwind RNA secondary structures as they enter the 48S. The structure also reveals conserved interactions between eIF4F and the 43S, probaby explaining how eIF4F can promote mRNA recruitment in all eukaryotes.
History
DepositionMay 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
5: Eukaryotic translation initiation factor 3 subunit E
6: Eukaryotic translation initiation factor 3 subunit F
7: Eukaryotic translation initiation factor 3 subunit G
8: Eukaryotic translation initiation factor 3 subunit H
9: 60S ribosomal protein L41
A: Eukaryotic translation initiation factor 3 subunit A
B: Eukaryotic translation initiation factor 3 subunit K
C: Eukaryotic translation initiation factor 3 subunit M
D: Eukaryotic translation initiation factor 2 subunit 1
E: Eukaryotic translation initiation factor 2 subunit 3
F: Eukaryotic translation initiation factor 3 subunit I
G: Eukaryotic translation initiation factor 1A, X-chromosomal
H: Eukaryotic translation initiation factor 5
I: Eukaryotic translation initiation factor 3 subunit B
J: Eukaryotic translation initiation factor 3 subunit C
K: Eukaryotic translation initiation factor 3 subunit L
L: 40S ribosomal protein S7
M: 40S ribosomal protein S27
N: 40S ribosomal protein S21
O: 40S ribosomal protein S2
P: 40S ribosomal protein S3a
Q: 40S ribosomal protein SA
R: 40S ribosomal protein S26
S: 40S ribosomal protein S6
T: 40S ribosomal protein S14
U: Eukaryotic translation initiation factor 2 subunit 2
V: 40S ribosomal protein S13
W: 18S rRNA
X: 40S ribosomal protein S11
Y: 40S ribosomal protein S4, X isoform
Z: 40S ribosomal protein S9
a: 40S ribosomal protein S23
b: 40S ribosomal protein S30
c: 40S ribosomal protein S15a
d: 40S ribosomal protein S8
e: 40S ribosomal protein S24
f: 40S ribosomal protein S5
g: 40S ribosomal protein S16
h: 40S ribosomal protein S3
i: 40S ribosomal protein S10
j: 40S ribosomal protein S15
k: Receptor of activated protein C kinase 1
l: 40S ribosomal protein S19
m: 40S ribosomal protein S25
n: Small ribosomal subunit protein uS13
o: 40S ribosomal protein S29
p: Ubiquitin-40S ribosomal protein S27a
q: 40S ribosomal protein S12
s: 40S ribosomal protein S28
v: 40S ribosomal protein S17
w: 40S ribosomal protein S20
x: Eukaryotic translation initiation factor 3 subunit D
y: tRNAiMet
z: mRNA
3: Eukaryotic initiation factor 4A-I
1: Eukaryotic initiation factor 4A-I
2: Eukaryotic translation initiation factor 4 gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,476,484148
Polymers2,474,19057
Non-polymers2,29491
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Eukaryotic translation initiation factor ... , 18 types, 18 molecules 5678ABCDEFGHIJKUx2

#1: Protein Eukaryotic translation initiation factor 3 subunit E / eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 ...eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 homolog / eIF-3 p48


Mass: 52281.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Eukaryotic translation initiation factor 3 subunit E
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF3E, EIF3S6, INT6 / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P60228
#2: Protein Eukaryotic translation initiation factor 3 subunit F / eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF- ...eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF-3-epsilon / eIF3 p47


Mass: 37593.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 3 subunit F
Source: (natural) Homo sapiens (human) / References: UniProt: O00303, ubiquitinyl hydrolase 1
#3: Protein Eukaryotic translation initiation factor 3 subunit G / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit ...eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Eukaryotic translation initiation factor 3 subunit 4 / eIF-3-delta / eIF3 p42 / eIF3 p44


Mass: 35662.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 3 subunit G
Source: (natural) Homo sapiens (human) / References: UniProt: O75821
#4: Protein Eukaryotic translation initiation factor 3 subunit H / eIF3h / Eukaryotic translation initiation factor 3 subunit 3 / eIF-3-gamma / eIF3 p40 subunit


Mass: 39979.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 3 subunit H
Source: (natural) Homo sapiens (human) / References: UniProt: O15372
#6: Protein Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 ...eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 / eIF3 p185


Mass: 166903.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 3 subunit A
Source: (natural) Homo sapiens (human) / References: UniProt: Q14152
#7: Protein Eukaryotic translation initiation factor 3 subunit K / eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / ...eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / PLAC-24 / eIF-3 p25 / eIF-3 p28


Mass: 25083.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 3 subunit K
Source: (natural) Homo sapiens (human) / References: UniProt: Q9UBQ5
#8: Protein Eukaryotic translation initiation factor 3 subunit M / eIF3m / Fetal lung protein B5 / hFL-B5 / PCI domain-containing protein 1


Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 3 subunit M
Source: (natural) Homo sapiens (human) / References: UniProt: Q7L2H7
#9: Protein Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit alpha / eIF-2alpha


Mass: 36161.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 2 subunit 1
Source: (natural) Homo sapiens (human) / References: UniProt: P05198
#10: Protein Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2gX


Mass: 51178.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 2 subunit 3
Source: (natural) Homo sapiens (human) / References: UniProt: P41091, protein-synthesizing GTPase
#11: Protein Eukaryotic translation initiation factor 3 subunit I / eIF3i / Eukaryotic translation initiation factor 3 subunit 2 / TGF-beta receptor-interacting ...eIF3i / Eukaryotic translation initiation factor 3 subunit 2 / TGF-beta receptor-interacting protein 1 / TRIP-1 / eIF-3-beta / eIF3 p36


Mass: 36543.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 3 subunit I
Source: (natural) Homo sapiens (human) / References: UniProt: Q13347
#12: Protein Eukaryotic translation initiation factor 1A, X-chromosomal / eIF-1A X isoform / Eukaryotic translation initiation factor 4C / eIF-4C


Mass: 16488.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Eukaryotic translation initiation factor 1A / Source: (gene. exp.) Homo sapiens (human) / Gene: EIF1AX, EIF1A, EIF4C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47813
#13: Protein Eukaryotic translation initiation factor 5


Mass: 49301.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Eukaryotic translation initiation factor 5 / Source: (gene. exp.) Homo sapiens (human) / Gene: EIF5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55010
#14: Protein Eukaryotic translation initiation factor 3 subunit B / eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / Prt1 homolog / hPrt1 / eIF-3-eta / ...eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / Prt1 homolog / hPrt1 / eIF-3-eta / eIF3 p110 / eIF3 p116


Mass: 92593.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 3 subunit B
Source: (natural) Homo sapiens (human) / References: UniProt: P55884
#15: Protein Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


Mass: 105503.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 3 subunit C
Source: (natural) Homo sapiens (human) / References: UniProt: Q99613
#16: Protein Eukaryotic translation initiation factor 3 subunit L / eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic ...eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic translation initiation factor 3 subunit E-interacting protein


Mass: 66803.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 3 subunit L
Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y262
#26: Protein Eukaryotic translation initiation factor 2 subunit 2 / Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


Mass: 38454.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 2 subunit 2
Source: (natural) Homo sapiens (human) / References: UniProt: P20042
#52: Protein Eukaryotic translation initiation factor 3 subunit D / eIF3d / Eukaryotic translation initiation factor 3 subunit 7 / eIF-3-zeta / eIF3 p66


Mass: 64060.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Eukaryotic translation initiation factor 3 subunit D
Source: (natural) Homo sapiens (human) / References: UniProt: O15371
#56: Protein Eukaryotic translation initiation factor 4 gamma 1


Mass: 155130.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Eukaryotic translation initiation factor 4 gamma / Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4G1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q04637

-
Protein/peptide , 1 types, 1 molecules 9

#5: Protein/peptide 60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 60S ribosomal protein L41 / Source: (natural) Homo sapiens (human) / References: UniProt: P62945

+
40S ribosomal protein ... , 30 types, 30 molecules LMNOPQRSTVXYZabcdefghijlmoqsvw

#17: Protein 40S ribosomal protein S7 / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS7 / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#18: Protein 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS27 / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#19: Protein 40S ribosomal protein S21 / Small ribosomal subunit protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS21 / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#20: Protein 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS5 / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#21: Protein 40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS1 / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#22: Protein 40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS2 / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#23: Protein 40S ribosomal protein S26 / Small ribosomal subunit protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS26 / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#24: Protein 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS6 / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#25: Protein 40S ribosomal protein S14 / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS11 / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#27: Protein 40S ribosomal protein S13 / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS15 / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#29: Protein 40S ribosomal protein S11 / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS17 / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#30: Protein 40S ribosomal protein S4, X isoform / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS4 / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#31: Protein 40S ribosomal protein S9 / Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS4 / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#32: Protein 40S ribosomal protein S23 / Small ribosomal subunit protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS12 / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#33: Protein 40S ribosomal protein S30 / Small ribosomal subunit protein eS30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS30 / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#34: Protein 40S ribosomal protein S15a / Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS8 / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#35: Protein 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS8 / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#36: Protein 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS24 / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#37: Protein 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS7 / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#38: Protein 40S ribosomal protein S16 / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS9 / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#39: Protein 40S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS3 / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#40: Protein 40S ribosomal protein S10 / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS10 / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#41: Protein 40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS19 / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#43: Protein 40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS19 / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#44: Protein 40S ribosomal protein S25 / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS25 / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#46: Protein 40S ribosomal protein S29 / Small ribosomal subunit protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS14 / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#48: Protein 40S ribosomal protein S12 / Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS12 / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#49: Protein 40S ribosomal protein S28 / Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS28 / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#50: Protein 40S ribosomal protein S17 / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS17 / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#51: Protein 40S ribosomal protein S20 / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS10 / Source: (natural) Homo sapiens (human) / References: UniProt: P60866

-
RNA chain , 3 types, 3 molecules Wyz

#28: RNA chain 18S rRNA


Mass: 555083.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 18S rRNA / Source: (natural) Homo sapiens (human)
#53: RNA chain tRNAiMet


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Human initiator Met-tRNA-i / Source: (synth.) Homo sapiens (human) / References: GenBank: 174924
#54: RNA chain mRNA


Mass: 67626.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: mRNA / Source: (synth.) Homo sapiens (human)

-
Protein , 4 types, 5 molecules knp31

#42: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Receptor of activated protein C kinase 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#45: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18 / Ke-3 / Ke3


Mass: 17630.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS13 / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#47: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS31 / Source: (natural) Homo sapiens (human) / References: UniProt: P62979
#55: Protein Eukaryotic initiation factor 4A-I


Mass: 46207.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Eukaryotic initiation factor 4A-I / Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60842

-
Non-polymers , 2 types, 91 molecules

#57: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#58: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 89 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human 48S translation initiation complex / Type: COMPLEX / Entity ID: #1-#56 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 47.88 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
2PHENIX1.19.2_4158:model refinement
3EPUimage acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 241389 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011127407
ELECTRON MICROSCOPYf_angle_d0.881181704
ELECTRON MICROSCOPYf_dihedral_angle_d14.96534643
ELECTRON MICROSCOPYf_chiral_restr0.04322569
ELECTRON MICROSCOPYf_plane_restr0.00616784

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more